Perfect.now if I wanted to use plotmesh with this, what would the variables be for x and y: plotmesh('x,y')On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
[aseg,M,mr] = load_mgh('aseg.mgz');
ind = find(aseg == 16);
that will give you the indices in the aseg volume of the voxels that have the brainstem label (16). Then you can do what you want with it. The label came from $FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Tue, 19 Jul 2016, Abbie McNulty wrote:
So say I load aseg.mgz into matlab and I want to extract the brainstem in matlab to plot its own volumetric mesh vs. the entire brain, how would I extract
the brainstem in matlab?
On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
but why not just load the aseg.mgz or whatever volume you are using directly into matlab? Then each structure has a different index that you can
extract with the find command
cheers
Bruce
On Tue, 19 Jul 2016, Abbie McNulty wrote:
I attached the page in the last message, maybe it didn't show. I guess they aren't called segmentations, but
isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/FreeviewWorkingWithData/FreeviewAnatomicalVolumes
This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a
.vtk file, I am not
converting anything
Abbie
On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
Hi Abbie
I'm not sure what page you mean. The segmentations start life as an .mgz file, so why convert them at all? Just load the
aseg.mgz (or whichever
segmentation you are interested in) into matlab directly
cheers
Bruce
On Tue, 19 Jul 2016, Abbie McNulty wrote:
Hi Bruce,
So when I'm at this page, I am separating the different parts of the brain so that in the 3D view they show up as their
own entity,
and I am trying to
individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file,
which makes
it difficult to upload
into matlab. Is there a way to convert this 3D brain piece as an .mgz file?
Thanks
On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote:
What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as
aseg.mgz
Cheers
Bruce
On Jul 18, 2016, at 1:19 PM, Abbie McNulty <amcnult1@stanford.edu> wrote:
So we were able to figure out how to segment the different parts of the brain using the bert sample, but have run
into another
problem.
I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh.
The volume
segment
saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so
that I can
import it
into matlab?
Thanks!
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Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
--
Abigail C. McNulty
Stanford University Class of 2018
B.A. Candidate in Bioengineering
Stanford Women's XC/ Track and Field
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The information in this e-mail is intended only for the person to whom it is
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http://www.partners.org/complianceline . If the e-mail was sent to you in error
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--Abigail C. McNultyStanford University Class of 2018B.A. Candidate in BioengineeringStanford Women's XC/ Track and Field